The creator of the font is responsible for such things. He should consider Simanim conflicts.
Anyway, you can fix them one by one, in the "Diacritics position" window. For example, select the Mercha and in diacritics window change its location. If it's a big file then this is an ant work, so think about buying more effective font.
I have had this same issue for a long time. There doesn't seem to be a fix for it.
Firstly, using the Diacritics position doesn't change anything when I try to do it manually.
Second of all, it is NOT something the creator of the font should consider. When I use the same exact text in the same exact font in Microsoft Word, the nikkud lines up correctly. Indesign messes it up, and I can't seem to find a fix for it.